Contacts of the strand formed by residues 49 - 55 (chain A) in PDB entry 2C4P
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with VAL 49 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36A THR* 3.3 30.5 - - + -
37A ILE 3.8 2.5 - - - -
38A MET* 4.7 13.0 - - - -
47A GLY 4.8 3.6 - - - +
48A GLY* 1.3 76.5 - - - +
50A PHE* 1.3 60.3 + - - +
51A PHE* 3.4 23.4 - - + -
71A THR* 3.5 9.4 + - - +
146A ALA* 2.7 33.0 + - - +
147A MET 5.5 4.0 - - - +
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Residues in contact with PHE 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A THR* 3.2 6.9 - - - -
37A ILE* 3.0 58.0 + - + -
39A GLY* 4.4 4.7 - - - -
45A TYR* 3.7 48.5 - + + -
48A GLY 4.1 8.5 - - - -
49A VAL* 1.3 74.4 - - - +
51A PHE* 1.3 62.4 + - - +
52A LEU* 3.3 3.2 - - + +
69A PHE* 3.1 33.2 - + + -
71A THR* 3.3 15.3 - - + -
72A LYS 3.8 17.9 - - - -
73A ILE* 3.9 13.5 - - + -
110A LEU* 4.9 2.7 - - + -
142A THR* 4.4 7.9 - - + -
146A ALA* 3.8 16.6 - - + -
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Residues in contact with PHE 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A GLN* 3.5 34.3 - - + -
35A ALA 3.4 3.4 - - - -
36A THR* 4.4 8.7 - - + -
49A VAL* 3.4 30.1 - - + -
50A PHE* 1.3 75.4 - - - +
52A LEU* 1.3 62.3 + - - +
69A PHE* 3.7 1.7 - - - -
70A THR* 2.7 49.0 + - + -
71A THR* 2.7 21.7 + - - +
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Residues in contact with LEU 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A GLN* 3.1 9.6 - - - +
35A ALA* 2.7 53.5 + - + +
37A ILE* 4.3 14.4 - - + +
50A PHE* 3.3 18.8 - - + +
51A PHE* 1.3 78.8 - - - +
53A THR* 1.3 61.6 + - - +
54A VAL* 5.0 4.7 - - + -
67A ILE* 5.5 3.6 - - + -
68A ALA 3.2 17.0 - - - +
69A PHE* 3.4 46.2 - - + -
70A THR* 4.5 2.0 - - - +
84A ILE* 3.9 8.1 - - + -
103A LEU* 5.8 5.4 - - + -
106A ILE* 5.8 2.5 - - + -
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Residues in contact with THR 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A HIS* 3.6 13.9 - - - -
33A TRP 3.6 5.0 + - - -
34A GLN* 4.4 2.7 - - - +
52A LEU* 1.3 74.1 - - - +
54A VAL* 1.3 60.0 + - - +
55A HIS* 3.4 30.4 + - - +
66A LYS 3.3 2.9 - - - +
67A ILE* 3.1 4.9 - - - -
68A ALA* 3.0 45.1 + - + +
70A THR* 4.4 13.0 + - - +
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Residues in contact with VAL 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A ALA* 5.6 1.3 - - + -
31A PHE 3.8 0.7 - - - +
32A HIS* 3.5 2.1 - - - -
33A TRP* 2.6 56.9 + - + +
35A ALA* 4.7 18.6 - - + -
52A LEU* 4.9 2.9 - - + -
53A THR* 1.3 75.5 - - - +
55A HIS* 1.3 63.8 + - - +
56A PHE* 3.7 23.5 + - + -
65A PRO* 4.0 14.6 - - + -
66A LYS 3.5 2.2 - - - -
67A ILE* 3.5 28.0 - - + -
99A VAL* 4.6 17.9 - - + -
103A LEU* 6.1 1.8 - - + -
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Residues in contact with HIS 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A PHE 3.5 4.3 - - - +
32A HIS* 3.3 38.2 + + - -
53A THR* 3.4 25.8 + - + +
54A VAL* 1.3 73.3 - - - +
56A PHE* 1.3 65.2 + - - +
57A PRO* 3.6 0.5 - - - +
65A PRO* 3.6 1.4 - - - +
66A LYS* 2.6 83.1 + - + +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il